The army on Thursday drove the militants out of the shrine, which had been used by them as a stronghold for months.
The militants had also desecrated parts of the shrine and set fire to the main building.
Sayyeda Sukeina (AS) is the daughter of Imam Hussein (AS), the third Shia imam and the grandson of the Prophet Muhammad (PBUH).
Elsewhere, in the western city of Homs, government troops killed at least 37 militants.
In recent weeks, the Syrian army has made major advances in its fight against the armed groups.
Earlier this week, the Syrian army units carried out similar operations against the militants in the countryside of the northwestern city of Idlib, killing 46 of them.
Syria has been gripped by deadly unrest since 2011. According to reports, the Western powers and their regional allies — especially Qatar, Saudi Arabia, and Turkey — are supporting the militants operating inside Syria.
A British defense study showed last year that about 100,000 militants, fragmented into 1,000 groups, were fighting in Syria against the government and people.
The extracts of the study by defense consultancy IHS Jane’s were published on September 16, 2013, revealing that some 10,000 militants were fighting for groups affiliated with al-Qaeda and the rest fighting for different militant groups.
According to the United Nations, more than 100,000 people have been killed and millions displaced in the foreign-backed militancy.